Complex 4aqy
Legend
Pocket colors by molecule type
RNA
Protein
DNA
These colors appear when a pocket is selected (the structure fades to show the pocket surface). Colors from the molecule-type palette (RNA / protein / DNA).
System information
| Experimental technique | X-ray |
| Experimental resolution | 3.50 |
| System mass | 797.51 kDa |
| Deposition year | 2012 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 4aqy |
| Reference | Matt Tanja, Ng Chyan Leong, Lang Kathrin, Sha Su-Hua, Akbergenov Rashid, Shcherbakov Dmitri, Meyer Martin, Duscha Stefan, Xie Jing, Dubbaka Srinivas R., Perez-Fernandez Déborah, Vasella Andrea, Ramakrishnan V., Schacht Jochen, Böttger Erik C.. 2012. Dissociation of antibacterial activity and aminoglycoside ototoxicity in the 4-monosubstituted 2-deoxystreptamine apramycin Proceedings of the National Academy of Sciences |
| Equivalence Class |
NR_all_65795.87
BGSU version: 4.52 |
Pockets List
Legend
Cell colors for SiteScore and D Score:
Favourable
Intermediate
Unfavourable
Not available
| Score | Threshold | Meaning |
|---|---|---|
| SiteScore | < 0.8 | Non-drug binding site |
| SiteScore | 0.8 – 1.0 | Potential drug binding site |
| SiteScore | > 1.0 | Promising binding site |
| D Score | < 0.83 | Undruggable |
| D Score | 0.83 – 0.98 | Difficult |
| D Score | > 0.98 | Druggable |
Tick a pocket below to highlight it in the 3D structure above.
| Compound | AM2 |
| Residue | . / 3001 |
| Chain | SH / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/A: rRNA |
| RNA family global | rRNA |
| Volume | 326.88 Å3 |
| Hydrophobicity | 0.202 |
| Hydrophilicity | 0.893 |
| Buriedness | 0.643 |
| Don/acc character | 2.240 |
| SiteScore | 1.035 |
| D Score | 0.898 |
| Kd | — |
| Compound | AM2 |
| Residue | . / 3002 |
| Chain | TH / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: rRNA |
| RNA family global | rRNA |
| Volume | 554.97 Å3 |
| Hydrophobicity | 0.077 |
| Hydrophilicity | 1.524 |
| Buriedness | 0.686 |
| Don/acc character | 0.688 |
| SiteScore | 1.142 |
| D Score | 0.855 |
| Kd | — |
| Compound | AM2 |
| Residue | . / 3003 |
| Chain | UH / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/A: rRNA |
| RNA family global | rRNA |
| Volume | 726.13 Å3 |
| Hydrophobicity | 0.090 |
| Hydrophilicity | 1.149 |
| Buriedness | 0.742 |
| Don/acc character | 2.304 |
| SiteScore | 1.179 |
| D Score | 1.011 |
| Kd | — |
| Compound | AM2 |
| Residue | . / 3004 |
| Chain | VH / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: rRNA |
| RNA family global | rRNA |
| Volume | 318.65 Å3 |
| Hydrophobicity | 0.220 |
| Hydrophilicity | 1.813 |
| Buriedness | 0.769 |
| Don/acc character | 0.668 |
| SiteScore | 0.751 |
| D Score | 0.350 |
| Kd | — |
| Compound | AM2 |
| Residue | . / 3005 |
| Chain | WH / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: rRNA |
| RNA family global | rRNA |
| Volume | 270.28 Å3 |
| Hydrophobicity | 0.065 |
| Hydrophilicity | 1.281 |
| Buriedness | 0.650 |
| Don/acc character | 0.891 |
| SiteScore | 1.011 |
| D Score | 0.776 |
| Kd | — |